Hi Dan,
I went to pod filters and a 4 into 1 exhaust (after using makeshift drag pipes).
I put in #120's. These worked very well for the drag pipes, but I notice a little mid-range hesitation with the 4-1 exhaust. I will probably have to try more sizes and play with it more. You may start with this size (or your own best guess), but you'll probably have to play with different sizes to see what works best. The jets aren't too expensive (around 2 and a half bucks a piece (you'll need 4)).
From what I gather, there are many factors that affect the engine's respiration. There are some rules of thumb in jet sizing, but in the end, it seems to boil down to trial and error.
Many folks use the spark-plug reading technique where you try to tell if the engine is rich or lean from how the plugs look. I would not be able to explain this technique adequately here. There are pictures of spark-plugs from various degrees of fuel/air mixtures to compare with. I even think my Clymers manual has some of these pictures.
Another thing to try is playing with the choke while riding (higher than idle RPMs). Basically, if the engine hesitates while riding, try the choke. Either the engine will perform better, worse, or no difference. If it runs better, then your mains may be too small (remember, you are choking the air intake). If it runs worse, then the mains may be too large. If there is no difference, then maybe the problem's not necessarily with the jetting.
Another thing you'll have to adjust is the slow jets. My '72 CB 750 has adjustment screws (I didn't have to change the stock #40 slow jets). Basically, as you idle down (such as when you're coming to a stop light), if you hear popping in the exhaust, then that means that there's fuel in the pipes that's cooking off. You'll want to adjust the slow jets so that you minimize this popping noise.
This discussion would not be complete without a mention of carburetor balancing (also called synchronizing). This involves hooking up vacuum gauges to the carbs and adjust the carbs so that they all pull about the same vacuum. I've seen some home-made 'manometers,' some inexpensive manufactured ones, and also gauges that are a slightly more expensive. Balancing is a little out of the scope of this post. It is not difficult, but when you attempt it, I suggest reading a more detailed description of the procedure than what I could try to give here. Perhaps someone in the forum has already explained it (not sure... I'm still new here).
Best of luck to you. It's a lot of fun playing with these bikes.